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Status |
Public on Jun 28, 2020 |
Title |
Hi-C_SCNT_PCC_rep2 |
Sample type |
SRA |
|
|
Source name |
SCNT PCC
|
Organism |
Mus musculus |
Characteristics |
cell type: SCNT PCC
|
Treatment protocol |
PCC SCNT embryos are collected one hour after the donor nucleus get injected into the enucleated MII oocytes. The reconstructed oocytes were incubated in CZB medium. The first polar body was removed by enucleation pipette on the micromanipulator, while the zona pellucida was gently removed by treatment with acid Tyrode’s solution (Sigma, Cat # T-1788) for several minutes.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
The DNA extraction follows Hi-C protocol Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
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Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
Instrument model |
HiSeq X Ten |
|
|
Description |
PCC_rep12_merge_allValidPairs.gz
|
Data processing |
Basecalls performed using CASAVA version 1.8 For Hi-C samples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size and 300Kb bin size wereused and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction. Genome_build: mm9 Supplementary_files_format_and_content: The validpair txt file indicates the paired interaction reads for each sample.
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Submission date |
Jun 28, 2020 |
Last update date |
Jun 30, 2020 |
Contact name |
Ke Zhang |
E-mail(s) |
zhangke16@mails.tsinghua.edu.cn
|
Organization name |
Tsinghua university
|
Department |
School of Life Sciences
|
Lab |
Wei Xie
|
Street address |
Haidian District
|
City |
Beijing |
State/province |
Beijing |
ZIP/Postal code |
100084 |
Country |
China |
|
|
Platform ID |
GPL21273 |
Series (1) |
GSE139430 |
Analysis of genome architecture during SCNT reveals a role of cohesin in impeding minor ZGA |
|
Relations |
BioSample |
SAMN15395535 |
SRA |
SRX8628808 |